• Mycobiology
• /
• v.49 no.4
• /
• pp.376-384
• /
• 2021

Agaricus bisporus is a popular edible mushroom that is cultivated worldwide. Due to its secondary homothallic nature, cultivated A. bisporus strains have low genetic diversity, and breeding novel strains is challenging. The aim of this study was to investigate the genetic diversity and population structure of globally collected A. bisporus strains using simple sequence repeat (SSR) markers. Agaricus bisporus strains were divided based on genetic distance-based groups and model-based subpopulations. The major allele frequency (MAF), number of genotypes (NG), number of alleles (NA), observed heterozygosity (HO), expected heterozygosity (HE), and polymorphic information content (PIC) were calculated, and genetic distance, population structure, genetic differentiation, and Hardy-Weinberg equilibrium (HWE) were assessed. Strains were divided into two groups by distance-based analysis and into three subpopulations by model-based analysis. Strains in subpopulations POP A and POP B were included in Group I, and strains in subpopulation POP C were included in Group II. Genetic differentiation between strains was 99%. Marker AB-gSSR-1057 in Group II and subpopulation POP C was confirmed to be in HWE. These results will enhance A. bisporus breeding programs and support the protection of genetic resources.

• Korean Journal of Breeding Science
• /
• v.43 no.1
• /
• pp.14-22
• /
• 2011

In this study, 15 simple sequence repeat (SSR) markers were used to analyze the population structure of 55 mungbean accessions (34 from South Asia, 20 from West Asia, 1 sample from East Asia). A total of 56 alleles were detected, with an average of 3.73 per locus. The mean of major allele frequency, expected heterozygosity and polymorphic information content for 15 SSR loci were 0.72, 0.07 and 0.33 respectively. The mean of major allele frequency was 0.79 for South Asia, and 0.74 for West Asia. The mean of genetic diversity and polymorphic information content were almost similar for South Asian and West Asian accessions (genetic diversity 0.35 and polymorphic information content 0.29). Model-based structure analysis revealed the presence of three clusters based on genetic distance. Accessions were clearly assigned to a single cluster in which >70% of their inferred ancestry was derived from one of the model-based populations. 47 accessions (85.56%) showed membership with the clusters and 8 accessions (14.54%) were categorized as admixture. The results could be used to understanding the genetic structure of mungbean cultivars from these regions and to support effective breeding programs to broaden the genetic basis of mungbean varieties.

• Genomics & Informatics
• /
• v.10 no.3
• /
• pp.133-144
• /
• 2012

Genetic admixture in human, the result of inter-marriage among people from different well-differentiated populations, has been extensively studied in the New World, where European colonization brought contact between peoples of Europe, Africa, and Asia and the Amerindian populations. In Asia, genetic admixing has been also prevalent among previously separated human populations. However, studies on admixed populations in Asia have been largely underrepresented in similar efforts in the New World. Here, I will provide an overview of population genomic studies that have been published to date on human admixture in Asia, focusing on population structure and population history.

• Journal of Life Science
• /
• v.30 no.11
• /
• pp.1007-1011
• /
• 2020

This study was conducted to analyze the genetic diversity and relationships that discriminate between Korean native black goat populations (Dangjin, Jangsu, Tongyoung, and Gyeongsang National University strains) and crossbred goats. Monomorphic single nucleotide polymorphisms (SNPs) in each strain were collected, and 133 common SNPs were selected for analysis. These 133 monomorphic SNPs showed differences in the genetic structure of the Korean native black goat and crossbred goats, and results from the principal component analysis (PCA) showed that the two can be clearly separated. Furthermore, analysis of the validation population comprising 70 individuals (Korean native black goats, n = 24; crossbred goats, n = 46) with the reference population showed that Korean native black goat strains and the reference population have the same genetic structure, and the crossbred goats shared only part of the genetic structure with the reference population. The result of the PCA analysis showed that the Korean native black goat strains form one population, whereas the foreign strains form another population which is more widely dispersed than the Korean native black goat strains. Thus, the results from this study can be used as baseline data for the conservation of genetic resources of Korean native black goat communities through utilization of monomorphic SNPs and for the introduction of exotic species for further improvement in genetic diversity. This study can also help reduce unnecessary inbreeding and gene flow between native strains.

• Parasites, Hosts and Diseases
• /
• v.55 no.5
• /
• pp.465-472
• /
• 2017

Recent trends of malaria in Thailand illustrate an increasing proportion of Plasmodium vivax, indicating the importance of P. vivax as a major causative agent of malaria. P. vivax malaria is usually considered a benign disease so the knowledge of this parasite has been limited, especially the genetic diversity and genetic structure of isolates from different endemic areas. The aim of this study was to examine the population genetics and structure of P. vivax isolates from 4 provinces with different malaria endemic settings in Thailand using 6 microsatellite markers. Total 234 blood samples from P. vivax mono-infected patients were collected. Strong genetic diversity was observed across all study sites; the expected heterozygosity values ranged from 0.5871 to 0.9033. Genetic variability in this study divided P. vivax population into 3 clusters; first was P. vivax isolates from Mae Hong Son and Kanchanaburi Provinces located on the western part of Thailand; second, Yala isolates from the south; and third, Chanthaburi isolates from the east. P. vivax isolates from patients having parasite clearance time (PCT) longer than 24 hr after the first dose of chloroquine treatment had higher diversity when compared with those having PCT within 24 hr. This study revealed a clear evidence of different population structure of P. vivax from different malaria endemic areas of Thailand. The findings provide beneficial information to malaria control programme as it is a useful tool to track the source of infections and current malaria control efforts.

• Animal Bioscience
• /
• v.34 no.7
• /
• pp.1105-1115
• /
• 2021

Objective: To conserve and utilize the genetic resources of a traditional Chinese indigenous pig breed, Liangshan pig, we assessed the genetic diversity, genetic structure, and genetic distance in this study. Methods: We used 50K single nucleotide polymorphism (SNP) chip for SNP detection of 139 individuals in the Liangshan Pig Conservation Farm. Results: The genetically closed conserved population consisted of five overlapping generations, and the total effective content of the population (Ne) was 15. The whole population was divided into five boar families and one non-boar family. Among them, the effective size of each generation subpopulation continuously decreased. However, the proportion of polymorphic markers (P_N) first decreased and then increased. The average genetic distance of these 139 Liangshan pigs was 0.2823±0.0259, and the average genetic distance of the 14 boars was 0.2723±0.0384. Thus, it can be deduced that the genetic distance changed from generation to generation. In the conserved population, 983 runs of homozygosity (ROH) were detected, and the majority of ROH (80%) were within 100 Mb. The inbreeding coefficient calculated based on ROH showed an average value of 0.026 for the whole population. In addition, the inbreeding coefficient of each generation subpopulation initially increased and then decreased. In the pedigree of the whole conserved population, the error rate of paternal information was more than 11.35% while the maternal information was more than 2.13%. Conclusion: This molecular study of the population genetic structure of Liangshan pig showed loss of genetic diversity during the closed cross-generation reproduction process. It is necessary to improve the mating plan or introduce new outside blood to ensure long-term preservation of Liangshan pig.

• Asian-Australasian Journal of Animal Sciences
• /
• v.15 no.6
• /
• pp.767-771
• /
• 2002

Breeding efficiencies were compared among three population schemes: a single population, a population with two subpopulations and a population with three sub-populations. A simulation experiment of selection was carried out for 10 generations with 20 replications each by comparing average breeding values and inbreeding coefficients among the three population schemes. Phenotypes of three traits were generated with a model comprising 36 loci, each with additive genetic effects and residuals distributed normally. Among the three population schemes, the single population scheme was definitely superior to the other two with regards to selection response and inbreeding. The multiple sub-population scheme was, however, considered to be an alternative population scheme when the difference in economic weights of the traits was small among the sub-populations, assuming moderate inbreeding depression for traits and crossbreeding. The scheme with two sub-populations had a higher genetic value than that with three subpopulations; however, the genetic values of the schemes were comparable when maternal heterosis was taken into account. The choice of population schemes may depend on the cost-sharing policy between the breeding population and the commercial population rather than just the breeding efficiency.

• Journal of Life Science
• /
• v.17 no.7 s.87
• /
• pp.882-888
• /
• 2007

Enzyme electrophoresis was used to estimate genetic diversity and population genetic structure of Pseudobagrus fulvidraco in Korea. Nine of the 14 loci (64.3%) showed detectable polymorphism. Genetic diversity at the population and species levels were 0.286 and 0.277, respectively. Analysis of fixation indices, calculated for all polymorphic loci in each population, showed a substantial deficit of hetero-zygotes relative to Hardy-Weinberg expectations. This deficit is expected that it is due to a limited effective number of individuals per population. The average $G_{ST}$ for polymorphic loci was 0.064, indicating that most (93.6%) of the genetic diversity occurred within populations. The indirect estimate of gene flow based on mean $G_{ST}$ was 3.67. Given limited gene flow is expected to diverge genetically due to drift and reduced populations. Most populations in our study experience annual, severe demo-graphic bottlenecks due to drought and floods.

• Asian-Australasian Journal of Animal Sciences
• /
• v.32 no.2
• /
• pp.176-182
• /
• 2019

Objective: This study was conducted to investigate basic information on genetic structure and characteristics of Limousin population in Hungary. Obtained results will be taken into consideration when adopting the new breeding strategy by the Association of Hungarian Limousin and Blonde d'Aquitaine Breeders (AHLBB). Methods: Genetic diversity and phylogenetic relationship of 3,443 Limousin cattle from 16 different herds were investigated by performing genotyping using 18 microsatellite markers. Amplified DNA was genotyped using an automated genetic analyzer. Results: Mean of effective alleles ($n_e$) of the populations was 3.77. Population C had the lowest number of effective alleles (3.01) and the lowest inbreeding coefficient ($F_{IS}$) value (-0.15). Principal component analysis of estimated genetic distance ($F_{ST}$) values (p<0.000) revealed two herds (C and E) distinct from the majority of other Limousin herds. The pairwise $F_{ST}$ values of population C compared to the others (0.066 to 0.120) fell into the range of moderate genetic distance: 0.050 to 0.150, while population E displayed also moderate genetic distance ($F_{ST}$ values in range 0.052 to 0.064) but only to six populations (G, H, J, L, N, and P). $F_{ST(C-E)}$ was 0.148, all other pairs -excluding C and E herds- displayed low genetic distance ($F_{ST}$<0.049). Population D, F, I, J, K, L, N, O, and P carried private alleles, which alleles belonged to 1.1% of the individuals. Most probable number of clusters (K) were 2 and 7 determined by Structure and BAPS software. Conclusion: This study showed useful genetic diversity and phylogenetic relationship data that can be utilized for the development of a new breeding strategy by AHLBB. The results presented could also contribute to the proper selection of animals for further whole genome scan studies of Limousins.

• Journal of Aquaculture
• /
• v.16 no.2
• /
• pp.69-75
• /
• 2003

Genetic variability and population structure of 11 natural ayu, Plecoglossus altivelis populations and one hatchery stock were assessed by starch gel electrophoretic analysis with 10 enzyme coding loci. Three loci were polymorphic (lower than 0.95 in major allele frequency) in natural populations,2 loci in hatchery stock. The average number of alleles per locus was 1.38. Observed heterozygosities ranged from 0.0235 to 0.088 (0.055 on the average) in natural population while 0.0925 in hatchery stock. The genetic distance among natural populations measured 0.000047-0.005407 and no significant differentiation was observed among them. On the other hand, a signifcant genetic distance was found between natural populations and the hatchery stock with measuring 0.002032-0.O08605. The results in this study suggest that the hatchery stock has diverged from natural populations, and also that careful to maintain sustainable and effective population size (parents number) should be made.